---
name: "gmx-scattering"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-scattering"
---

# gmx-scattering(1)

Calculate small angle scattering profiles for SANS or SAXS

## NAME

gmx-scattering - Calculate small angle scattering profiles for SANS or SAXS

## SYNOPSIS

```
gmx scattering [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
             [-n [<.ndx>]] [-o [<.xvg>]] [-b <time>] [-e <time>]
             [-dt <time>] [-tu <enum>] [-fgroup <selection>]
             [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
             [-selrpos <enum>] [-seltype <enum>] [-sel <selection>]
             [-startq <real>] [-endq <real>] [-qspacing <real>]
             [-binwidth <real>] [-mc-coverage <real>] [-seed <int>]
             [-[no]norm] [-[no]mc] [-scattering-type <enum>]
```

## DESCRIPTION

**gmx scattering** calculates SANS and SAXS scattering curves using Debye method.

The scattering intensity, I(q), as a function of scattering angle q with averaging over frames.

Note that this is a new implementation of the SANS/SAXS utilities added in GROMACS 2024. If you need the old ones, use **gmx sans-legacy** or **gmx saxs-legacy**.

## OPTIONS

Options to specify input files:

- **-f \[\<.xtc/.trr/...\>\] (traj.xtc) (Optional)**

  Input trajectory or single configuration: *xtc* *trr* *cpt* *gro* *g96* *pdb* *tng*

- **-s \[\<.tpr/.gro/...\>\] (topol.tpr) (Optional)**

  Input structure: *tpr* *gro* *g96* *pdb* brk ent

- **-n \[\<.ndx\>\] (index.ndx) (Optional)**

  Extra index groups

Options to specify output files:

- **-o \[\<.xvg\>\] (scattering.xvg) (Optional)**

  scattering intensity as a function of q

Other options:

- **-b \<time\> (0)**

  First frame (ps) to read from trajectory

- **-e \<time\> (0)**

  Last frame (ps) to read from trajectory

- **-dt \<time\> (0)**

  Only use frame if t MOD dt == first time (ps)

- **-tu \<enum\> (ps)**

  Unit for time values: fs, ps, ns, us, ms, s

- **-fgroup \<selection\>**

  Atoms stored in the trajectory file (if not set, assume first N atoms)

- **-xvg \<enum\> (xmgrace)**

  Plot formatting: xmgrace, xmgr, none

- **-\[no\]rmpbc (yes)**

  Make molecules whole for each frame

- **-\[no\]pbc (yes)**

  Use periodic boundary conditions for distance calculation

- **-sf \<file\>**

  Provide selections from files

- **-selrpos \<enum\> (atom)**

  Selection reference positions: atom, res\_com, res\_cog, mol\_com, mol\_cog, whole\_res\_com, whole\_res\_cog, whole\_mol\_com, whole\_mol\_cog, part\_res\_com, part\_res\_cog, part\_mol\_com, part\_mol\_cog, dyn\_res\_com, dyn\_res\_cog, dyn\_mol\_com, dyn\_mol\_cog

- **-seltype \<enum\> (atom)**

  Default selection output positions: atom, res\_com, res\_cog, mol\_com, mol\_cog, whole\_res\_com, whole\_res\_cog, whole\_mol\_com, whole\_mol\_cog, part\_res\_com, part\_res\_cog, part\_mol\_com, part\_mol\_cog, dyn\_res\_com, dyn\_res\_cog, dyn\_mol\_com, dyn\_mol\_cog

- **-sel \<selection\>**

  Selection for Scattering calculation

- **-startq \<real\> (0)**

  smallest q value (1/nm)

- **-endq \<real\> (2)**

  largest q value (1/nm)

- **-qspacing \<real\> (0.01)**

  spacing of q values (1/nm)

- **-binwidth \<real\> (0.1)**

  Bin width (nm) for P(r)

- **-mc-coverage \<real\> (0.2)**

  coverage of Monte Carlo (%)

- **-seed \<int\> (2023)**

  random seed for Monte Carlo

- **-\[no\]norm (no)**

  normalize scattering intensities

- **-\[no\]mc (yes)**

  use Monte Carlo to scattering intensities

- **-scattering-type \<enum\> (sans)**

  Scattering type: saxs, sans

## SEE ALSO

**[gmx(1)](/gmx/1.md)**

More information about GROMACS is available at \<*http://www.gromacs.org/*\>.

## COPYRIGHT

2025, GROMACS development team